Spirochetes as a group comprise a large portion of the subgingival plaque bacterial flora involved in periodontal diseases. Although spirochetes have been implicated as etiologic agents in periodontal diseases, their role in these diseases is not understood. The lack of knowledge concerning the role of spirochetes in oral ecology relates to difficulty in culturing and enumerating individual spirochete species. Molecular techniques will be developed for rapid quantitation of the relative abundances of individual spirochete species from subgingival plaque samples. This is a critical step towards understanding the roles of spirochetes in periodontal diseases. The molecular approach under development involves a coupled PCR-fluorescent oligonucleotide probe analysis to simultaneously estimate the relative abundances of several individual oral spirochete species, the total spirochete population, and the total eubacterial population in a subgingival plaque sample. The overall procedure will be rapid, providing data in less than two days from the time of sample procurement, and large numbers of samples can be processed simultaneously. The coupling of PCR technology and automated fluorescent oligonucleotide analytical technology allows for a sensitive, highly specific, simultaneous-multispecies analysis. This is a first step towards designing meaningful clinical studies where well-defined periodontal disease states or disease activity are correlated with abundances of specific spirochetes. The long-term objective is to use the PCR-fluorescent probe procedure to develop appropriate ecological studies aimed at understanding oral spirochetes as they relate to periodontal diseases. Also, it is anticipated that the analytical technique under development may have wide applicability to studies of other bacteria in natural samples.